Hey Greg H,
to me it sounds like the rig was updated or has changed somehow in a way that the names of your controllers changed and maya can't attatch the right animation curves to the handles anymore. Maybe you changed the prefix for all controllers. If the rig is referenced and animation allready startet renaming the controllers in the rig file will kill your animation. What you can do: rollback the rig to an earlier stage, before the renaming.
The reference edit setAttr has nothing to do with animation its just about setting one value on an attribut (like a pose) without keying the attribute. You should watch out for connectAttr edits. You also can check the outliner for your lost functioncurves. Tunr Off "Show DAG Objects Only" then you should be able to find the unconnected animamationCurves (they have an icon looking like a grapheditor with some blue and yellow functionCurves). They have its names according to the attributes they where connected with, i.e.: T:turt_r_knee_anim.translateX should have been connected with T:turt_r_knee_anim_translateX animCurve ..so you may be able to see what namechange happend in the rig.... if that is the problem.
If that was not the problem and the names are still right you might be able to reconnect the animationCurves via name and a smart script so T:turt_r_knee_anim_translateX.output will be connected to T:turt_r_knee_anim.translateX, T:turt_r_knee_anim_translateY.output to T:turt_r_knee_anim.translateY and so on...
good luck...